Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

2C38

RNase PH core of the archaeal exosome in complex with A5 RNA

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000177	cellular_component	cytoplasmic exosome (RNase complex)
A	0000178	cellular_component	exosome (RNase complex)
A	0005515	molecular_function	protein binding
A	0005737	cellular_component	cytoplasm
A	0006401	biological_process	RNA catabolic process
A	0016075	biological_process	rRNA catabolic process
A	0035925	molecular_function	mRNA 3'-UTR AU-rich region binding
B	0000175	molecular_function	3'-5'-RNA exonuclease activity
B	0000177	cellular_component	cytoplasmic exosome (RNase complex)
B	0000178	cellular_component	exosome (RNase complex)
B	0000956	biological_process	nuclear-transcribed mRNA catabolic process
B	0003723	molecular_function	RNA binding
B	0004518	molecular_function	nuclease activity
B	0004527	molecular_function	exonuclease activity
B	0005515	molecular_function	protein binding
B	0005737	cellular_component	cytoplasm
B	0006401	biological_process	RNA catabolic process
B	0010467	biological_process	gene expression
B	0016075	biological_process	rRNA catabolic process
B	0016787	molecular_function	hydrolase activity
B	0016896	molecular_function	RNA exonuclease activity, producing 5'-phosphomonoesters
B	1902494	cellular_component	catalytic complex
C	0000177	cellular_component	cytoplasmic exosome (RNase complex)
C	0000178	cellular_component	exosome (RNase complex)
C	0005515	molecular_function	protein binding
C	0005737	cellular_component	cytoplasm
C	0006401	biological_process	RNA catabolic process
C	0016075	biological_process	rRNA catabolic process
C	0035925	molecular_function	mRNA 3'-UTR AU-rich region binding
D	0000175	molecular_function	3'-5'-RNA exonuclease activity
D	0000177	cellular_component	cytoplasmic exosome (RNase complex)
D	0000178	cellular_component	exosome (RNase complex)
D	0000956	biological_process	nuclear-transcribed mRNA catabolic process
D	0003723	molecular_function	RNA binding
D	0004518	molecular_function	nuclease activity
D	0004527	molecular_function	exonuclease activity
D	0005515	molecular_function	protein binding
D	0005737	cellular_component	cytoplasm
D	0006401	biological_process	RNA catabolic process
D	0010467	biological_process	gene expression
D	0016075	biological_process	rRNA catabolic process
D	0016787	molecular_function	hydrolase activity
D	0016896	molecular_function	RNA exonuclease activity, producing 5'-phosphomonoesters
D	1902494	cellular_component	catalytic complex
E	0000177	cellular_component	cytoplasmic exosome (RNase complex)
E	0000178	cellular_component	exosome (RNase complex)
E	0005515	molecular_function	protein binding
E	0005737	cellular_component	cytoplasm
E	0006401	biological_process	RNA catabolic process
E	0016075	biological_process	rRNA catabolic process
E	0035925	molecular_function	mRNA 3'-UTR AU-rich region binding
F	0000175	molecular_function	3'-5'-RNA exonuclease activity
F	0000177	cellular_component	cytoplasmic exosome (RNase complex)
F	0000178	cellular_component	exosome (RNase complex)
F	0000956	biological_process	nuclear-transcribed mRNA catabolic process
F	0003723	molecular_function	RNA binding
F	0004518	molecular_function	nuclease activity
F	0004527	molecular_function	exonuclease activity
F	0005515	molecular_function	protein binding
F	0005737	cellular_component	cytoplasm
F	0006401	biological_process	RNA catabolic process
F	0010467	biological_process	gene expression
F	0016075	biological_process	rRNA catabolic process
F	0016787	molecular_function	hydrolase activity
F	0016896	molecular_function	RNA exonuclease activity, producing 5'-phosphomonoesters
F	1902494	cellular_component	catalytic complex
G	0000177	cellular_component	cytoplasmic exosome (RNase complex)
G	0000178	cellular_component	exosome (RNase complex)
G	0005515	molecular_function	protein binding
G	0005737	cellular_component	cytoplasm
G	0006401	biological_process	RNA catabolic process
G	0016075	biological_process	rRNA catabolic process
G	0035925	molecular_function	mRNA 3'-UTR AU-rich region binding
H	0000175	molecular_function	3'-5'-RNA exonuclease activity
H	0000177	cellular_component	cytoplasmic exosome (RNase complex)
H	0000178	cellular_component	exosome (RNase complex)
H	0000956	biological_process	nuclear-transcribed mRNA catabolic process
H	0003723	molecular_function	RNA binding
H	0004518	molecular_function	nuclease activity
H	0004527	molecular_function	exonuclease activity
H	0005515	molecular_function	protein binding
H	0005737	cellular_component	cytoplasm
H	0006401	biological_process	RNA catabolic process
H	0010467	biological_process	gene expression
H	0016075	biological_process	rRNA catabolic process
H	0016787	molecular_function	hydrolase activity
H	0016896	molecular_function	RNA exonuclease activity, producing 5'-phosphomonoesters
H	1902494	cellular_component	catalytic complex
I	0000177	cellular_component	cytoplasmic exosome (RNase complex)
I	0000178	cellular_component	exosome (RNase complex)
I	0005515	molecular_function	protein binding
I	0005737	cellular_component	cytoplasm
I	0006401	biological_process	RNA catabolic process
I	0016075	biological_process	rRNA catabolic process
I	0035925	molecular_function	mRNA 3'-UTR AU-rich region binding
J	0000175	molecular_function	3'-5'-RNA exonuclease activity
J	0000177	cellular_component	cytoplasmic exosome (RNase complex)
J	0000178	cellular_component	exosome (RNase complex)
J	0000956	biological_process	nuclear-transcribed mRNA catabolic process
J	0003723	molecular_function	RNA binding
J	0004518	molecular_function	nuclease activity
J	0004527	molecular_function	exonuclease activity
J	0005515	molecular_function	protein binding
J	0005737	cellular_component	cytoplasm
J	0006401	biological_process	RNA catabolic process
J	0010467	biological_process	gene expression
J	0016075	biological_process	rRNA catabolic process
J	0016787	molecular_function	hydrolase activity
J	0016896	molecular_function	RNA exonuclease activity, producing 5'-phosphomonoesters
J	1902494	cellular_component	catalytic complex
K	0000177	cellular_component	cytoplasmic exosome (RNase complex)
K	0000178	cellular_component	exosome (RNase complex)
K	0005515	molecular_function	protein binding
K	0005737	cellular_component	cytoplasm
K	0006401	biological_process	RNA catabolic process
K	0016075	biological_process	rRNA catabolic process
K	0035925	molecular_function	mRNA 3'-UTR AU-rich region binding
L	0000175	molecular_function	3'-5'-RNA exonuclease activity
L	0000177	cellular_component	cytoplasmic exosome (RNase complex)
L	0000178	cellular_component	exosome (RNase complex)
L	0000956	biological_process	nuclear-transcribed mRNA catabolic process
L	0003723	molecular_function	RNA binding
L	0004518	molecular_function	nuclease activity
L	0004527	molecular_function	exonuclease activity
L	0005515	molecular_function	protein binding
L	0005737	cellular_component	cytoplasm
L	0006401	biological_process	RNA catabolic process
L	0010467	biological_process	gene expression
L	0016075	biological_process	rRNA catabolic process
L	0016787	molecular_function	hydrolase activity
L	0016896	molecular_function	RNA exonuclease activity, producing 5'-phosphomonoesters
L	1902494	cellular_component	catalytic complex
M	0000177	cellular_component	cytoplasmic exosome (RNase complex)
M	0000178	cellular_component	exosome (RNase complex)
M	0005515	molecular_function	protein binding
M	0005737	cellular_component	cytoplasm
M	0006401	biological_process	RNA catabolic process
M	0016075	biological_process	rRNA catabolic process
M	0035925	molecular_function	mRNA 3'-UTR AU-rich region binding
N	0000175	molecular_function	3'-5'-RNA exonuclease activity
N	0000177	cellular_component	cytoplasmic exosome (RNase complex)
N	0000178	cellular_component	exosome (RNase complex)
N	0000956	biological_process	nuclear-transcribed mRNA catabolic process
N	0003723	molecular_function	RNA binding
N	0004518	molecular_function	nuclease activity
N	0004527	molecular_function	exonuclease activity
N	0005515	molecular_function	protein binding
N	0005737	cellular_component	cytoplasm
N	0006401	biological_process	RNA catabolic process
N	0010467	biological_process	gene expression
N	0016075	biological_process	rRNA catabolic process
N	0016787	molecular_function	hydrolase activity
N	0016896	molecular_function	RNA exonuclease activity, producing 5'-phosphomonoesters
N	1902494	cellular_component	catalytic complex
O	0000177	cellular_component	cytoplasmic exosome (RNase complex)
O	0000178	cellular_component	exosome (RNase complex)
O	0005515	molecular_function	protein binding
O	0005737	cellular_component	cytoplasm
O	0006401	biological_process	RNA catabolic process
O	0016075	biological_process	rRNA catabolic process
O	0035925	molecular_function	mRNA 3'-UTR AU-rich region binding
P	0000175	molecular_function	3'-5'-RNA exonuclease activity
P	0000177	cellular_component	cytoplasmic exosome (RNase complex)
P	0000178	cellular_component	exosome (RNase complex)
P	0000956	biological_process	nuclear-transcribed mRNA catabolic process
P	0003723	molecular_function	RNA binding
P	0004518	molecular_function	nuclease activity
P	0004527	molecular_function	exonuclease activity
P	0005515	molecular_function	protein binding
P	0005737	cellular_component	cytoplasm
P	0006401	biological_process	RNA catabolic process
P	0010467	biological_process	gene expression
P	0016075	biological_process	rRNA catabolic process
P	0016787	molecular_function	hydrolase activity
P	0016896	molecular_function	RNA exonuclease activity, producing 5'-phosphomonoesters
P	1902494	cellular_component	catalytic complex
Q	0000177	cellular_component	cytoplasmic exosome (RNase complex)
Q	0000178	cellular_component	exosome (RNase complex)
Q	0005515	molecular_function	protein binding
Q	0005737	cellular_component	cytoplasm
Q	0006401	biological_process	RNA catabolic process
Q	0016075	biological_process	rRNA catabolic process
Q	0035925	molecular_function	mRNA 3'-UTR AU-rich region binding
R	0000175	molecular_function	3'-5'-RNA exonuclease activity
R	0000177	cellular_component	cytoplasmic exosome (RNase complex)
R	0000178	cellular_component	exosome (RNase complex)
R	0000956	biological_process	nuclear-transcribed mRNA catabolic process
R	0003723	molecular_function	RNA binding
R	0004518	molecular_function	nuclease activity
R	0004527	molecular_function	exonuclease activity
R	0005515	molecular_function	protein binding
R	0005737	cellular_component	cytoplasm
R	0006401	biological_process	RNA catabolic process
R	0010467	biological_process	gene expression
R	0016075	biological_process	rRNA catabolic process
R	0016787	molecular_function	hydrolase activity
R	0016896	molecular_function	RNA exonuclease activity, producing 5'-phosphomonoesters
R	1902494	cellular_component	catalytic complex
S	0000177	cellular_component	cytoplasmic exosome (RNase complex)
S	0000178	cellular_component	exosome (RNase complex)
S	0005515	molecular_function	protein binding
S	0005737	cellular_component	cytoplasm
S	0006401	biological_process	RNA catabolic process
S	0016075	biological_process	rRNA catabolic process
S	0035925	molecular_function	mRNA 3'-UTR AU-rich region binding
T	0000175	molecular_function	3'-5'-RNA exonuclease activity
T	0000177	cellular_component	cytoplasmic exosome (RNase complex)
T	0000178	cellular_component	exosome (RNase complex)
T	0000956	biological_process	nuclear-transcribed mRNA catabolic process
T	0003723	molecular_function	RNA binding
T	0004518	molecular_function	nuclease activity
T	0004527	molecular_function	exonuclease activity
T	0005515	molecular_function	protein binding
T	0005737	cellular_component	cytoplasm
T	0006401	biological_process	RNA catabolic process
T	0010467	biological_process	gene expression
T	0016075	biological_process	rRNA catabolic process
T	0016787	molecular_function	hydrolase activity
T	0016896	molecular_function	RNA exonuclease activity, producing 5'-phosphomonoesters
T	1902494	cellular_component	catalytic complex
U	0000177	cellular_component	cytoplasmic exosome (RNase complex)
U	0000178	cellular_component	exosome (RNase complex)
U	0005515	molecular_function	protein binding
U	0005737	cellular_component	cytoplasm
U	0006401	biological_process	RNA catabolic process
U	0016075	biological_process	rRNA catabolic process
U	0035925	molecular_function	mRNA 3'-UTR AU-rich region binding
V	0000175	molecular_function	3'-5'-RNA exonuclease activity
V	0000177	cellular_component	cytoplasmic exosome (RNase complex)
V	0000178	cellular_component	exosome (RNase complex)
V	0000956	biological_process	nuclear-transcribed mRNA catabolic process
V	0003723	molecular_function	RNA binding
V	0004518	molecular_function	nuclease activity
V	0004527	molecular_function	exonuclease activity
V	0005515	molecular_function	protein binding
V	0005737	cellular_component	cytoplasm
V	0006401	biological_process	RNA catabolic process
V	0010467	biological_process	gene expression
V	0016075	biological_process	rRNA catabolic process
V	0016787	molecular_function	hydrolase activity
V	0016896	molecular_function	RNA exonuclease activity, producing 5'-phosphomonoesters
V	1902494	cellular_component	catalytic complex
W	0000177	cellular_component	cytoplasmic exosome (RNase complex)
W	0000178	cellular_component	exosome (RNase complex)
W	0005515	molecular_function	protein binding
W	0005737	cellular_component	cytoplasm
W	0006401	biological_process	RNA catabolic process
W	0016075	biological_process	rRNA catabolic process
W	0035925	molecular_function	mRNA 3'-UTR AU-rich region binding
X	0000175	molecular_function	3'-5'-RNA exonuclease activity
X	0000177	cellular_component	cytoplasmic exosome (RNase complex)
X	0000178	cellular_component	exosome (RNase complex)
X	0000956	biological_process	nuclear-transcribed mRNA catabolic process
X	0003723	molecular_function	RNA binding
X	0004518	molecular_function	nuclease activity
X	0004527	molecular_function	exonuclease activity
X	0005515	molecular_function	protein binding
X	0005737	cellular_component	cytoplasm
X	0006401	biological_process	RNA catabolic process
X	0010467	biological_process	gene expression
X	0016075	biological_process	rRNA catabolic process
X	0016787	molecular_function	hydrolase activity
X	0016896	molecular_function	RNA exonuclease activity, producing 5'-phosphomonoesters
X	1902494	cellular_component	catalytic complex

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CL B 301

Chain	Residue
B	ARG99
B	GLY137
B	SER138
B	ARG139
B	AMP404

site_id	AC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CL D 301

Chain	Residue
D	ARG99
D	GLY137
D	SER138
D	ARG139

site_id	AC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CL F 301

Chain	Residue
F	GLY137
F	SER138
F	ARG139
F	AMP404

site_id	AC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CL H 301

Chain	Residue
H	ARG99
H	GLY137
H	SER138
H	ARG139
H	AMP404

site_id	AC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CL J 301

Chain	Residue
J	ARG99
J	GLY137
J	SER138
J	ARG139
J	AMP404

site_id	AC6
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CL L 301

Chain	Residue
L	ARG99
L	GLY137
L	SER138
L	ARG139

site_id	AC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CL N 301

Chain	Residue
N	ARG99
N	GLY137
N	SER138
N	ARG139
N	AMP404

site_id	AC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CL P 301

Chain	Residue
P	ARG2
P	ARG99
P	GLY137
P	SER138
P	ARG139

site_id	AC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE CL R 301

Chain	Residue
R	ARG99
R	GLY137
R	SER138
R	ARG139

site_id	BC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CL T 301

Chain	Residue
R	ARG2
T	ARG99
T	GLY137
T	SER138
T	ARG139

site_id	BC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CL V 301

Chain	Residue
V	ARG99
V	GLY137
V	SER138
V	ARG139
V	AMP404

site_id	BC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE CL X 301

Chain	Residue
X	ARG99
X	GLY137
X	SER138
X	ARG139
X	AMP404

site_id	BC4
Number of Residues	4
Details	BINDING SITE FOR RESIDUE AMP B 401

Chain	Residue
A	TYR75
A	LEU84
B	ARG98
B	AMP402

site_id	BC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE AMP B 402

Chain	Residue
A	ARG112
A	ARG119
B	ARG98
B	AMP401
B	AMP403

site_id	BC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE AMP B 403

Chain	Residue
A	ARG112
A	ARG116
B	ASP182
B	AMP402
B	AMP404

site_id	BC7
Number of Residues	12
Details	BINDING SITE FOR RESIDUE AMP B 404

Chain	Residue
B	MET83
B	THR88
B	ARG99
B	ALA134
B	ALA136
B	SER138
B	ARG139
B	GLU179
B	ASP182
B	ASP188
B	CL301
B	AMP403

site_id	BC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE AMP F 401

Chain	Residue
E	TYR75
E	LEU84
F	ARG98
F	AMP402

site_id	BC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE AMP F 402

Chain	Residue
E	ARG112
E	ARG119
F	ARG98
F	AMP401
F	AMP403

site_id	CC1
Number of Residues	4
Details	BINDING SITE FOR RESIDUE AMP F 403

Chain	Residue
E	ARG112
F	ASP182
F	AMP402
F	AMP404

site_id	CC2
Number of Residues	11
Details	BINDING SITE FOR RESIDUE AMP F 404

Chain	Residue
F	SER138
F	ARG139
F	GLU179
F	ASP182
F	ASP188
F	CL301
F	AMP403
F	THR88
F	ARG99
F	ALA134
F	ALA136

site_id	CC3
Number of Residues	7
Details	BINDING SITE FOR RESIDUE AMP H 401

Chain	Residue
G	TYR75
G	LEU84
G	ILE85
G	ASP115
G	ARG119
H	ARG98
H	AMP402

site_id	CC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE AMP H 402

Chain	Residue
G	ARG112
G	ARG119
H	ARG98
H	AMP401
H	AMP403

site_id	CC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE AMP H 403

Chain	Residue
G	ARG112
H	ASP182
H	AMP402
H	AMP404

site_id	CC6
Number of Residues	12
Details	BINDING SITE FOR RESIDUE AMP H 404

Chain	Residue
H	THR88
H	ARG99
H	ALA134
H	ASP135
H	ALA136
H	SER138
H	ARG139
H	GLU179
H	ASP182
H	ASP188
H	CL301
H	AMP403

site_id	CC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE AMP J 401

Chain	Residue
I	TYR75
I	LEU84
I	ILE85
J	ARG98
J	AMP402

site_id	CC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE AMP J 402

Chain	Residue
I	ARG112
I	ASP115
J	ARG98
J	AMP401
J	AMP403

site_id	CC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE AMP J 403

Chain	Residue
I	ARG112
J	ASP182
J	AMP402
J	AMP404

site_id	DC1
Number of Residues	13
Details	BINDING SITE FOR RESIDUE AMP J 404

Chain	Residue
J	MET83
J	THR88
J	ARG99
J	ALA134
J	ASP135
J	ALA136
J	SER138
J	ARG139
J	GLU179
J	ASP182
J	ASP188
J	CL301
J	AMP403

site_id	DC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE AMP N 401

Chain	Residue
M	TYR75
M	LEU84
M	ILE85
N	ARG98
N	AMP402

site_id	DC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE AMP N 402

Chain	Residue
M	ARG112
M	ASP115
N	ARG98
N	AMP401
N	AMP403

site_id	DC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE AMP N 403

Chain	Residue
M	ARG112
M	ARG116
N	ASP182
N	AMP402
N	AMP404

site_id	DC5
Number of Residues	11
Details	BINDING SITE FOR RESIDUE AMP N 404

Chain	Residue
N	MET83
N	THR88
N	ARG99
N	ALA136
N	SER138
N	ARG139
N	GLU179
N	ASP182
N	ASP188
N	CL301
N	AMP403

site_id	DC6
Number of Residues	7
Details	BINDING SITE FOR RESIDUE AMP V 401

Chain	Residue
U	TYR75
U	LEU84
U	ILE85
U	ASP115
U	ARG119
V	ARG98
V	AMP402

site_id	DC7
Number of Residues	6
Details	BINDING SITE FOR RESIDUE AMP V 402

Chain	Residue
U	ARG112
U	ASP115
U	ARG119
V	ARG98
V	AMP401
V	AMP403

site_id	DC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE AMP V 403

Chain	Residue
U	ARG112
U	ARG116
V	ASP182
V	AMP402
V	AMP404

site_id	DC9
Number of Residues	12
Details	BINDING SITE FOR RESIDUE AMP V 404

Chain	Residue
V	THR88
V	ARG99
V	ALA134
V	ASP135
V	ALA136
V	SER138
V	ARG139
V	GLU179
V	ASP182
V	ASP188
V	CL301
V	AMP403

site_id	EC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE AMP X 401

Chain	Residue
W	TYR75
W	LEU84
X	AMP402

site_id	EC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE AMP X 402

Chain	Residue
W	ARG112
W	ASP115
W	ARG119
X	ARG98
X	AMP401
X	AMP403

site_id	EC3
Number of Residues	5
Details	BINDING SITE FOR RESIDUE AMP X 403

Chain	Residue
W	ARG112
X	ASP182
X	MET183
X	AMP402
X	AMP404

site_id	EC4
Number of Residues	12
Details	BINDING SITE FOR RESIDUE AMP X 404

Chain	Residue
X	MET83
X	THR88
X	ARG99
X	ALA134
X	ASP135
X	ALA136
X	SER138
X	ARG139
X	GLU179
X	ASP182
X	CL301
X	AMP403

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)